bartlettSelection {ClassifyR} | R Documentation

## Selection of Differential Variability with Bartlett Statistic

### Description

Ranks features by largest Bartlett statistic and chooses the features which have best resubstitution performance.

### Usage

      ## S4 method for signature 'matrix'
    bartlettSelection(measurements, classes, ...)
      ## S4 method for signature 'DataFrame'
    bartlettSelection(measurements, classes, datasetName,
                      trainParams, predictParams, resubstituteParams,
                      selectionName = "Bartlett Test", verbose = 3)
      ## S4 method for signature 'MultiAssayExperiment'
    bartlettSelection(measurements, targets, ...)

### Arguments

`measurements` | Either a `matrix`, `DataFrame` or `MultiAssayExperiment` containing the training data. For a `matrix`, the rows are features, and the columns are samples.
`classes` | Either a vector of class labels of class `factor` of the same length as the number of samples in `measurements` or if the measurements are of class `DataFrame` a character vector of length 1 containing the column name in `measurement` is also permitted. Not used if `measurements` is a `MultiAssayExperiment` object.
`targets` | If `measurements` is a `MultiAssayExperiment`, the names of the data tables to be used. `"clinical"` is also a valid value and specifies that numeric variables from the clinical data table will be used.
`...` | Variables not used by the `matrix` nor the `MultiAssayExperiment` method which are passed into and used by the `DataFrame` method.
`datasetName` | A name for the data set used. Stored in the result.
`trainParams` | A container of class `TrainParams` describing the classifier to use for training.
`predictParams` | A container of class `PredictParams` describing how prediction is to be done.
`resubstituteParams` | An object of class `ResubstituteParams` describing the performance measure to consider and the numbers of top features to try for resubstitution classification.
`selectionName` | A name to identify this selection method by. Stored in the result.
`verbose` | Default: 3. A number between 0 and 3 for the amount of progress messages to give. This function only prints progress messages if the value is 3.

### Details

The calculation of the test statistic is performed by the `bartlett.test` function from the `stats` package.

Data tables which consist entirely of non-numeric data cannot be analysed. If `measurements` is an object of class `MultiAssayExperiment`, the factor of sample classes must be stored in the DataFrame accessible by the `colData` function with column name `"class"`.

### Value

An object of class `SelectResult` or a list of such objects, if the classifier which was used for determining the specified performance metric made a number of prediction varieties.

### Author(s)

Dario Strbenac

### Examples

      # Samples in one class with differential variability to other class.
      # First 20 genes are DV.
      genesRNAmatrix <- sapply(1:25, function(sample) c(rnorm(100, 9, 1)))
      moreVariable <- sapply(1:25, function(sample) rnorm(20, 9, 5))
      genesRNAmatrix <- cbind(genesRNAmatrix, rbind(moreVariable,
                              sapply(1:25, function(sample) rnorm(80, 9, 1))))
      colnames(genesRNAmatrix) <- paste("Sample", 1:50)
      rownames(genesRNAmatrix) <- paste("Gene", 1:100)
      genesSNPmatrix <- matrix(sample(c("None", "Missense"), 250, replace = TRUE),
                               ncol = 50)
      colnames(genesSNPmatrix) <- paste("Sample", 1:50)
      rownames(genesSNPmatrix) <- paste("Gene", 1:5)
      classes <- factor(rep(c("Poor", "Good"), each = 25))
      names(classes) <- paste("Sample", 1:50)
      genesDataset <- MultiAssayExperiment(list(RNA = genesRNAmatrix, SNP = genesSNPmatrix),
                                           colData = DataFrame(class = classes))
      # Wait for update to MultiAssayExperiment wideFormat function.
      trainIDs <- paste("Sample", c(1:20, 26:45))
      genesDataset <- subtractFromLocation(genesDataset, training = trainIDs,
                                           targets = "RNA") # Exclude SNP data.

      resubstituteParams <- ResubstituteParams(nFeatures = seq(10, 100, 10),
                                               performanceType = "balanced error",
                                               better = "lower")
      bartlettSelection(genesDataset, datasetName = "Example", targets = "RNA",
                        trainParams = TrainParams(fisherDiscriminant),
                        predictParams = PredictParams(NULL),
                        resubstituteParams = resubstituteParams)

[Package ClassifyR version 2.14.0 Index]